Molecular Dynamics Study of Thymidine Phosphorylase from E. coli in the Apo Form and in Complexes with Substrates

Models of E. coli thymidine phosphorylase in complexes with the substrates — the complex with phosphate and the complex with phosphate and thymidine — were obtained by molecular docking calculations. The influence of the substrates on domain movements in the dimeric thymidine phosphorylase molecule...

Full description

Saved in:
Bibliographic Details
Published in:Crystallography reports 2019, Vol.64 (1), p.98-104
Main Authors: Sidorov-Biryukov, D. D., Podshivalov, D. D., Timofeev, V. I., Zhukhlistova, N. E., Kuranova, I. P.
Format: Article
Language:English
Subjects:
Binding sites
Computer simulation
Crystallography and Scattering Methods
E coli
Molecular docking
Molecular dynamics
Physics
Physics and Astronomy
Structure of Macromolecular Compounds
Substrates
Thymidine
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Models of E. coli thymidine phosphorylase in complexes with the substrates — the complex with phosphate and the complex with phosphate and thymidine — were obtained by molecular docking calculations. The influence of the substrates on domain movements in the dimeric thymidine phosphorylase molecule was probed by molecular dynamics simulations. The two subunits were shown to function asynchronously. In the thymidine phosphorylase/phosphate and thymidine phosphorylase/phosphate/thymidine complexes, phosphate is more weakly bound in the active site and moves away from the phosphate-binding site during the 60-ns trajectory, whereas thymidine remains in the active site but undergoes conformational changes.
ISSN:1063-7745
1562-689X
DOI:10.1134/S1063774518060287